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Jmel H, Sarno S, Giuliani C, Boukhalfa W, Abdelhak S, Luiselli D, Kefi R. Genetic diversity of variants involved in drug response among Tunisian and Italian populations toward personalized medicine. Sci Rep 2024; 14:5842. [PMID: 38462643 PMCID: PMC10925599 DOI: 10.1038/s41598-024-55239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Adverse drug reactions (ADR) represent a significant contributor to morbidity and mortality, imposing a substantial financial burden. Genetic ancestry plays a crucial role in drug response. The aim of this study is to characterize the genetic variability of selected pharmacogenes involved with ADR in Tunisians and Italians, with a comparative analysis against global populations. A cohort of 135 healthy Tunisians and 737 Italians were genotyped using a SNP array. Variants located in 25 Very Important Pharmacogenes implicated in ADR were extracted from the genotyping data. Distribution analysis of common variants in Tunisian and Italian populations in comparison to 24 publicly available worldwide populations was performed using PLINK and R software. Results from Principle Component and ADMIXTURE analyses showed a high genetic similarity among Mediterranean populations, distinguishing them from Sub-Saharan African and Asian populations. The Fst comparative analysis identified 27 variants exhibiting significant differentiation between the studied populations. Among these variants, four SNPs rs622342, rs3846662, rs7294, rs5215 located in SLC22A1, HMGCR, VKORC1 and KCNJ11 genes respectively, are reported to be associated with ethnic variability in drug responses. In conclusion, correlating the frequencies of genotype risk variants with their associated ADRs would enhance drug outcomes and the implementation of personalized medicine in the studied populations.
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Affiliation(s)
- Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Genetic Typing DNA Service Pasteur Institute, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Donata Luiselli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage (DBC), University of Bologna, Ravenna, Italy
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia.
- University of Tunis El Manar, Tunis, Tunisia.
- Genetic Typing DNA Service Pasteur Institute, Institut Pasteur de Tunis, Tunis, Tunisia.
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Genetic analysis of pharmacogenomic VIP variants in the Wa population from Yunnan Province of China. BMC Genom Data 2021; 22:51. [PMID: 34798807 PMCID: PMC8605568 DOI: 10.1186/s12863-021-00999-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background The variation of drug responses and target does among individuals is mostly determined by genes. With the development of pharmacogenetics and pharmacogenomics, the differences in drug response between different races seem to be mainly caused by the genetic diversity of pharmacodynamics and pharmacokinetics genes. Very important pharmacogenetic (VIP) variants mean that genes or variants play important and vital roles in drug response, which have been listed in pharmacogenomics databases, such as Pharmacogenomics Knowledge Base (PharmGKB). The information of Chinese ethnic minorities such as the Wa ethnic group is scarce. This study aimed to uncover the significantly different loci in the Wa population in Yunnan Province of China from the perspective of pharmacogenomics, to provide a theoretical basis for the future medication guidance, and to ultimately achieve the best treatment in the future. Results In this study, we recruited 200 unrelated healthy Wa adults from the Yunnan province of China, selected 52 VIP variants from the PharmGKB for genotyping. We also compared the genotype frequency and allele distribution of VIP variants between Wa population and the other 26 populations from the 1000 Genomes Project (http://www.1000Genomes.org/). Next, χ2 test was used to determine the significant points between these populations. The study results showed that compared with the other 26 population groups, five variants rs776746 (CYP3A5), rs4291 (ACE), rs3093105 (CYP4F2), rs1051298 (SLC19A1), and rs1065852 (CYP2D6) had higher frequencies in the Wa population. The genotype frequencies rs4291-TA, rs3093105-CA, rs1051298-AG and rs1065852-GA were higher than those of the other populations, and the allele distributions of rs4291-T and rs3093105-C were significantly different. Additionally, the difference between the Wa ethnic group and East Asian populations, such as CDX, CHB, and CHS, was the smallest. Conclusions Our research results show that there is a significant difference in the distribution of VIP variants between the Wa ethnic group and the other 26 populations. The study results will have an effect on supplementing the pharmacogenomics information for the Wa population and providing a theoretical basis for individualised medication for the Wa population. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00999-8.
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He C, Peng L, Xing S, Li D, Wang L, Jin T. Population Genetic Difference of Pharmacogenomic VIP Variants in the Tibetan Population. Pharmgenomics Pers Med 2021; 14:1027-1040. [PMID: 34429635 PMCID: PMC8379641 DOI: 10.2147/pgpm.s316711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Genetic variation influences drug reaction or adverse prognosis. The purpose of this research was to genotype very important pharmacogenetic (VIP) variants in the Tibetan population. METHODS AND MATERIALS Blood samples from 200 Tibetans were randomly collected and 59 VIP variants were genotyped, and then compared our data to 26 other populations in the 1000 project to further analyze and identify significant difference. RESULTS The results showed that on comparing with most of the 26 populations from the 1000 project, rs4291 (ACE), rs1051296 (SLC19A1) and rs1065852 (CYP2D6) significantly differed in the Tibetan population. Furthermore, three significant loci were related to drug response. In addition, the allele frequency of Tibetans least differed from that of East Asian populations, and most differed from that of Americans. CONCLUSION Three significant loci of variation ACE rs4291, SLC19A1 rs1051296 and CYP2D6 rs1065852 were associated with drug response. This result will contribute to improving the information of the Tibetan in the pharmacogenomics database, and providing a theoretical basis for clinical individualised drug use in Tibetans.
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Affiliation(s)
- Chunjuan He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Linna Peng
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Shishi Xing
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Dandan Li
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Li Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Tianbo Jin
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
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Genetic variation of pharmacogenomic VIP variants in Zhuang nationality of southern China. THE PHARMACOGENOMICS JOURNAL 2020; 21:60-68. [PMID: 32699276 DOI: 10.1038/s41397-020-0177-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 05/18/2020] [Accepted: 07/09/2020] [Indexed: 11/09/2022]
Abstract
Drug gene polymorphisms are strongly associated with disease. Previous studies have shown that the frequency of drug genes varies in different populations. At present, there are no reports about the polymorphism of the drug genome in the Zhuang population in southern China. This study conducted a pharmacogenomics study on the Zhuang population in southern China. Therefore, we conducted genotyping on 105 Zhuang samples, and compared the genotyping results with those of other 11 ethnic groups after statistical analysis. Our results show that, compared with the 11 populations in the HapMap data set, the differences between the CYP2E1 rs2070676 and CYP2D6 rs1065852 of the Zhuang nationality are the largest. This study fills in the blank of the drug genome information of the Zhuang nationality in southern China. The two sites of Rs2070676 (CYP2E1) and rs1065852 (CYP2D6) provide a reliable basis for the prediction of the efficacy of certain drugs. Its main purpose is to provide theoretical basis for safe drug use in the Zhuang region of southern China.
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AL-Eitan LN, Al-Maqableh HW, Mohammad NN, Khair Hakooz NM, Dajani RB. Genetic Analysis of Pharmacogenomic VIP Variants of ABCB1, VDR and TPMT Genes in an Ethnically Isolated Population from the North Caucasus Living in Jordan. Curr Drug Metab 2020; 21:307-317. [DOI: 10.2174/1389200221666200505081139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 01/11/2023]
Abstract
Background:
Differences in individual responses to the same medications remarkably differ among
populations. A number of genes that play integral roles in drug responses have been designated as very important
pharmacogenes (VIP), as they are responsible for differences in drug safety, efficacy, and adverse drug reactions
among certain ethnic groups. Identifying the polymorphic distribution of VIP in a range of ethnic groups will be
conducive to population-based personalized medicine.
Objective:
The aim of the current study is to identify the polymorphic distribution of VIP regarding the Chechen
minority group from Jordan and compare their allele frequencies with other populations.
Methods:
A total of 131 unrelated Chechen individuals from Jordan were randomly recruited for blood collection.
Identification of allelic and genotypic frequencies of eleven VIP variants within the genes of interest (ABCB1, VDR
and TPMT) was carried out by means of the MassARRAY®System (iPLEX GOLD).
Results:
Within ABCB1, we found that the minor allele frequencies of the rs1128503 (A: 0.43), rs2032582 (A: 0.43),
rs1045642 (A: 0.43). For VDR, the minor allele frequencies of rs11568820 (T: 0.18), rs1540339 (T: 0.30), rs1544410
(T: 0.41), rs2228570 (T: 0.24), rs3782905 (C: 0.28) and rs7975232 (C: 0.45). Finally, the minor allele frequencies for
the TPMT rs1142345 and rs1800460 polymorphisms were found to be (C: 0.02) and (T: 0.01), respectively.
Conclusion:
Significant differences in allelic frequencies of eleven ABCB1, VDR and TPMT VIP variants were
found between Jordanian Chechens and other populations. In our study, most populations that are similar to
Chechens are those from South Asian, European (Finnish) and European, including: Utah residents with Northern
and Western European ancestry, Toscani in Italia, Mexican ancestry in Los Angeles and Circassian from Jordan. The
level of similarity between Chechens and those populations means that they might have shared high levels of gene
flow in the past. The results obtained in this study will contribute to the worldwide pharmacogenomic databases and
provide valuable information for future studies and better individualized treatments.
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Affiliation(s)
- Laith Naser AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | | | - Namarg Nawwaf Mohammad
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Nancy Mohamed Khair Hakooz
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Rana Basem Dajani
- Department of Biology and Biotechnology, Hashemite University, Zarqa 13133, Jordan
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Genetic Polymorphisms of Pharmacogenes among the Genetically Isolated Circassian Subpopulation from Jordan. J Pers Med 2020; 10:jpm10010002. [PMID: 31935801 PMCID: PMC7151588 DOI: 10.3390/jpm10010002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/21/2019] [Accepted: 12/30/2019] [Indexed: 12/11/2022] Open
Abstract
Several genetic variants have been identified that cause variation among different populations and even within individuals of a similar descent. This leads to interindividual variations in the optimal dose of the drug that is required to sustain the treatment efficiency. In this study, 56 single nucleotide polymorphisms (SNPs) within several pharmacogenes were analyzed in 128 unrelated subjects from a genetically isolated group of Circassian people living in Jordan. We also compared these variant distributions to other ethnic groups that are available at two databases (Genome 1000 and eXAC). Our results revealed that the distribution of allele frequencies within genes among Circassians in Jordan showed similarities and disparities when compared to other populations. This study provides a powerful base for clinically relevant SNPs to enhance medical research and future pharmacogenomic studies. Rare variants detected in isolated populations can significantly guide to novel loci involved in the development of clinically relevant traits.
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Al-Eitan LN, Mohammad NN, Al-Maqableh HW, Hakooz NM, Dajani RB. Genetic Polymorphisms of Pharmacogenomic VIP Variants in the Circassian Subpopulation from Jordan. Curr Drug Metab 2019; 20:674-681. [PMID: 31362667 DOI: 10.2174/1389200220666190729124000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/27/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND It has been suggested that genetic variation within candidate pharmacogenes contributes to the differences in drug safety and efficacy as well as risk of adverse drug reactions among different ethnic groups. Illustrating the polymorphic distribution of Very Important Pharmacogenes (VIPs) in various ethnic groups will contribute to the development of personalized medicine for those populations. OBJECTIVE The present study aimed to identify the polymorphic distribution of VIPs in the Circassian subpopulation of Jordan and compare their allele frequencies with those of other populations. METHODS A total of 130 healthy and unrelated Circassian adults from Jordan were randomly recruited and genotyped for eleven VIP variants within the thiopurine S-methyltransferase (TPMT), ATP-binding cassette, sub-family B, member 1 (ABCB1), and vitamin D receptor (VDR) genes via Sequenom's MassARRAY® genotyping platform (iPLEX GOLD). RESULTS Our data on the allelic frequencies of the investigated VIP variants were compared to those of 18 other populations, comprising 11 HapMap populations, 6 Exome Aggregation Consortium populations, and the Chechen- Jordanian population from Jordan. Circassian-Jordanians were found to most resemble the African, Chechen- Jordanian, European (Finnish), European (non-Finnish), and South-Asian populations. CONCLUSION Circassians from Jordan significantly differ from other populations in terms of the allelic frequencies of selected VIP variants. The present findings constitute the first set of pharmacogenetic data for Circassian population from Jordan, providing a basis for safe drug administration that may be useful in diagnosing and treating diseases in this ethnic group.
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Affiliation(s)
- Laith N Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.,Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Namarg N Mohammad
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Haneen W Al-Maqableh
- Department of Biology and Biotechnology, Hashemite University, Zarqa 13133, Jordan
| | - Nancy M Hakooz
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Rana B Dajani
- Department of Biology and Biotechnology, Hashemite University, Zarqa 13133, Jordan.,Radcliffe Institute for Advanced Studies, Harvard University, Cambridge, 02138 MA, United States
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Zhang J, Wang H, Niu G, Liu Y, Wang Y, Zhang L, Pei Y, Zhu H, Dai P, Chen C. Deciphering DMET genetic data: comprehensive assessment of Northwestern Han, Tibetan, Uyghur populations and their comparison to eleven 1000 genome populations. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 46:S1176-S1185. [PMID: 30688101 DOI: 10.1080/21691401.2018.1533849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We investigated the allele frequencies of drug absorption, distribution, metabolism and elimination (ADME)-related drug-metabolizing enzymes and transporters (DMET) genes in the Northwestern Han, Tibetan and Uyghur populations and compared the related genes in these three populations with those in eleven 1000 Genome populations. We examined 1936 single nucleotide polymorphisms of 225 DMET genes involved in ADME processes and found 732, 679 and 804 sites were polymorphic in Han, Tibetan and Uyghur. Tibetan differed from Han in only four sites (p < .05), whereas Uyghur differed from Han and Tibetan in 24 and 21 sites, respectively (p < .05). The distributions of 1058 genotyping data of 245 individuals from Han, Tibetan and Uyghur were compared with 1207 other individuals from the eleven 1000 Genomes populations. The top four populations in Han that exhibited the smallest pairwise Fst values were CHB, Tibetan, CHD and JPT; those in Tibetan were Han, CHB, Uyghur and CHD; and those in Uyghur were Han, Tibetan, GIH and CEU. MEGA results revealed that CHB, CHD, JPT, Han, Tibetan and Uyghur were grouped in cluster 1. GIH, MEX, CEU and TSI were grouped in cluster 2. MKK, ASW, LWK and YRI were grouped in cluster 3.
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Affiliation(s)
- Jiayi Zhang
- a College of Life Science , Northwest University , Xi'an , China
| | - Huijuan Wang
- a College of Life Science , Northwest University , Xi'an , China
| | - Geng Niu
- a College of Life Science , Northwest University , Xi'an , China
| | - Yongkang Liu
- a College of Life Science , Northwest University , Xi'an , China
| | - Yanxia Wang
- a College of Life Science , Northwest University , Xi'an , China
| | - Lirong Zhang
- a College of Life Science , Northwest University , Xi'an , China
| | - Yanrui Pei
- a College of Life Science , Northwest University , Xi'an , China
| | - Hongli Zhu
- a College of Life Science , Northwest University , Xi'an , China.,b National Engineering Research Center for Miniaturized Detection Systems , Northwest University , Xi'an , China
| | - Penggao Dai
- a College of Life Science , Northwest University , Xi'an , China.,b National Engineering Research Center for Miniaturized Detection Systems , Northwest University , Xi'an , China
| | - Chao Chen
- a College of Life Science , Northwest University , Xi'an , China.,b National Engineering Research Center for Miniaturized Detection Systems , Northwest University , Xi'an , China
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Zhang C, Jiang X, Chen W, Li Q, Yun F, Yang X, Dai R, Cheng Y. Population genetic difference of pharmacogenomic VIP gene variants in the Lisu population from Yunnan Province. Medicine (Baltimore) 2018; 97:e13674. [PMID: 30593137 PMCID: PMC6314765 DOI: 10.1097/md.0000000000013674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Individual differences in drug clinical response are related to pharmacogenomics. The genetic variation of drug-metabolizing enzymes, drug receptors, and their downstream protein genes is the main factor causing individual differences in drug response. The genetic backgrounds among different ethnic groups are quite different. In this study, we aimed to detect the distribution difference of genotype frequency in very important pharmacogenetic (VIP) gene variants in the Lisu.Using the chi-squared test, we compared the genotype frequencies of the VIP variants in 105 Lisu people with those in 26 populations from the 1000 Genome project separately. Bonferroni's multiple adjustment was also conducted (P < .05/(26*49)). Moreover, Arlequin v3.5 and Structure v2.3.4 software were used to analyze the genetic distance and genetic structure.There were 9, 9, 11, 12, 11, 11, 9, 17, 13, 13, 16, 5, 3, 5, 3, 4, 17, 14, 16, 17, 16, 10, 13, 12, 10, and 9 single nucleotide polymorphisms that differed in frequency distribution, when Lisu people compared with the 26 populations separately. Only CYP2E1 rs2070676 was different in the Lisu population compared with the 26 groups from the 1000 Genome project. PTGS2 rs5275 and CYP2D6 rs1065852 were different in the Lisu population compared with most of the populations. Additionally, genetic backgrounds of Lisu and Han Chinese in Beijing were closest according to the lowest F-statistics value and resemblance in genetic structures.Our results complete the information of the Lisu population in pharmacogenomics database.
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Affiliation(s)
- Chan Zhang
- Department of Blood Transfusion, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology
| | - Xiaochun Jiang
- Department of Blood Transfusion, The Third People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Wanlu Chen
- Department of Blood Transfusion, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology
| | - Qi Li
- Department of Blood Transfusion, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology
| | - Fubin Yun
- Department of Blood Transfusion, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology
| | - Xin Yang
- Department of Blood Transfusion, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology
| | - Run Dai
- Department of Blood Transfusion, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology
| | - Yujing Cheng
- Department of Blood Transfusion, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology
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Li B, Wang L, Lei L, Zhang M, Niu F, Chen P, Jin T. Genetic polymorphisms of pharmacogenomic VIP variants in the Lisu population of southwestern China: A cohort study. Medicine (Baltimore) 2018; 97:e12231. [PMID: 30235667 PMCID: PMC6160020 DOI: 10.1097/md.0000000000012231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/14/2018] [Indexed: 11/26/2022] Open
Abstract
Pharmacogenomic studies of different ethnic or racial groups have been used to develop personalized therapies specific to subjects. This study aimed to identify the distribution differences of very important pharmacogenetic (VIP) variants between the Lisu population from southwestern China and other ethnic groups.Eighty VIP variants in 37 genes were selected from the pharmacogenomic knowledge base (PharmGKB), and compared with genotype data of the Lisu population then compared with other 11 populations from the HapMap dataset and previously published data including Miao, Li, Deng, Sherpa, Lhoba, Tibetan, Kirghiz, Tajik, Mongol, Shaanxi Han ethnic, and Uygur populations.VDR rs1540339, MTHFR rs1801131, P2RY1 rs701265, and PTGS2 rs689466 were significantly different between Lisu and 11 HapMap populations. ANKK1 rs1800497 was the least statistical significant locus among selected single nucleotide polymorphisms. In addition, genetic background of Lisu was strongly closest to Shaanxi Han ethnic cohort, and followed by Chinese in metropolitan Denver population based on population structure and F-statistics analyses.Our results showed significant interethnic differences between Lisu and other populations, which will give useful information for prospective studies and better individualized treatments.
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Affiliation(s)
- Bin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Li Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Lingyu Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Mingxiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Fanglin Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Peng Chen
- Institution of Basic Medical Science, Xi’an Medical University, Xi’an
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
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Jmel H, Romdhane L, Ben Halima Y, Hechmi M, Naouali C, Dallali H, Hamdi Y, Shan J, Abid A, Jamoussi H, Trabelsi S, Chouchane L, Luiselli D, Abdelhak S, Kefi R. Pharmacogenetic landscape of Metabolic Syndrome components drug response in Tunisia and comparison with worldwide populations. PLoS One 2018; 13:e0194842. [PMID: 29652911 PMCID: PMC5898725 DOI: 10.1371/journal.pone.0194842] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/09/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic variation is an important determinant affecting either drug response or susceptibility to adverse drug reactions. Several studies have highlighted the importance of ethnicity in influencing drug response variability that should be considered during drug development. Our objective is to characterize the genetic variability of some pharmacogenes involved in the response to drugs used for the treatment of Metabolic Syndrome (MetS) in Tunisia and to compare our results to the worldwide populations. A set of 135 Tunisians was genotyped using the Affymetrix Chip 6.0 genotyping array. Variants located in 24 Very Important Pharmacogenes (VIP) involved in MetS drug response were extracted from the genotyping data. Analysis of variant distribution in Tunisian population compared to 20 worldwide populations publicly available was performed using R software packages. Common variants between Tunisians and the 20 investigated populations were extracted from genotyping data. Multidimensional screening showed that Tunisian population is clustered with North African and European populations. The greatest divergence was observed with the African and Asian population. In addition, we performed Inter-ethnic comparison based on the genotype frequencies of five VIP biomarkers. The genotype frequencies of the biomarkers rs3846662, rs1045642, rs7294 and rs12255372 located respectively in HMGCR, ABCB1, VKORC1 and TCF7L2 are similar between Tunisian, Tuscan (TSI) and European (CEU). The genotype frequency of the variant rs776746 located in CYP3A5 gene is similar between Tunisian and African populations and different from CEU and TSI. The present study shows that the genetic make up of the Tunisian population is relatively complex in regard to pharmacogenes and reflects previous historical events. It is important to consider this ethnic difference in drug prescription in order to optimize drug response to avoid serious adverse drug reactions. Taking into account similarities with other neighboring populations, our study has an impact not only on the Tunisian population but also on North African population which are underrepresented in pharmacogenomic studies.
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Affiliation(s)
- Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Yosra Ben Halima
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Chokri Naouali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Abdelmajid Abid
- Department of external consultation, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Henda Jamoussi
- Department of external consultation, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Sameh Trabelsi
- Clinical Pharmacology Service, National Pharmacovigilance Center, Tunis, Tunisia
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Donata Luiselli
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- * E-mail: ,
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Li J, Guo C, Yan M, Niu F, Chen P, Li B, Jin T. Genetic polymorphisms in very important pharmacogenomic variants in the Zhuang ethnic group of Southwestern China: A cohort study in the Zhuang population. Medicine (Baltimore) 2018; 97:e0559. [PMID: 29703042 PMCID: PMC5944516 DOI: 10.1097/md.0000000000010559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Pharmacogenomics, the study of the role of genetics in drug response, has recently become a focal point of research. Previous studies showed that genes associated with drug detoxification vary among different populations. However, pharmacogenomic information of the Zhuang ethnic group is scarce. The aim of the present study was to screen members of the Zhuang ethnicity in southwestern China for genotype frequencies of very important pharmacogenomic (VIP) variants and to determine the differences between the Zhuang ethnicity and other human populations.We genotyped 80 variants of VIP genes in 100 unrelated healthy Zhuang adults from the Yunnan province of China. Next, we analyzed the genotyping data with Structure and F-statistics (Fst).We compared our data with those of other populations using the HapMap data set, and observed that the frequency distribution of Zhuang population in Yunnan closely resembles that of JPT. Furthermore, population structure and Fst analysis showed that the Zhuang population is closely related to the Shaanxi Han population with respect to genetic background.Our study supplements existing information on Zhuang population pharmacogenomics and provides an extensive overview for developing personalized medicine.
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Affiliation(s)
- Jing Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education
| | - Chenghao Guo
- Xi’an 21st Century Precision Medicine Research Institute Co. Ltd
| | - Mengdan Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education
| | - Fanglin Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education
| | - Peng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education
| | - Bin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
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13
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Qi G, Li D, Zhang X. Genetic variation of cytochrome P450 in Uyghur Chinese population. Drug Metab Pharmacokinet 2017; 33:55-60. [PMID: 29233455 DOI: 10.1016/j.dmpk.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/29/2016] [Accepted: 02/24/2017] [Indexed: 12/01/2022]
Abstract
Interindividual and interethnic variability of drug responses could be attributed to the differences of genetic polymorphisms in the drug metabolizing enzymes and transporters genes among the populations. Here we reviewed the studies of genetic variations in Uyghur Chinese of fifteen CYP450 genes including CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP2J2, CYP2W1, CYP3A4, CYP3A5, CYP4A11, and CYP17A1, which totally covered 277 variants. We also collected the data of 277 variants covered in our study in two extensive population sequencing projects, the International HapMap Project (Hap-Map) and the 1000 Genomes Project and compared them with the data of Uyghur Chinese. The results suggested that remarkable differences of variants allele frequencies of CYP450 genes were existed among Uyghur Chinese and other world populations and drug doses should be adjusted clinically in Uyghur in contrast to Han Chinese and Caucasians.
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Affiliation(s)
- Guangzhao Qi
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Duolu Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaojian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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14
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Jin T, Zhao R, Shi X, He N, He X, Ouyang Y, Wang H, Wang B, Kang L, Yuan D. Genetic polymorphisms study of pharmacogenomic VIP variants in Han ethnic of China's Shaanxi province. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2016; 46:27-35. [PMID: 27414743 DOI: 10.1016/j.etap.2016.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/21/2016] [Accepted: 06/26/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Multiple factors include genetic and non-genetic interactions induce to different drug response among different individuals. Lots of researches proved that different frequencies of genetic variants exists different ethnic groups. The aim of this study was to screen Han volunteers in Shaanxi for VIP gene polymorphisms. MATERIALS AND METHODS We genotyped 80 Very Important Pharmacogenes (VIP) (selected from the PharmGKB database) in 192 unrelated, healthy Han ethnic adults from Shaanxi, the northwest of China, and then analyzed genotyping data wtih Structure and F-statistics (Fst) analysis. RESULTS We compared our data with 15 other populations (Deng, Kyrgyz, Tajik, Uygur and 11 HapMap populations), and found the frequency distribution of Han population in Shaanxi is most similar with CHB. Also, Structure and Fst showed that Shaanxi Han has a closest genetic background with CHB. CONCLUSIONS Our study have supplemented the Han Chinese data related to pharmacogenomics and illustrated differences in genotypic frequencies of selected VIP variants' among the Han population and 15 other populations.
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Affiliation(s)
- Tianbo Jin
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, China; Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Ruimin Zhao
- Otorhinolaryngological, Head and Neck Surgery Department, School of Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Xugang Shi
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, China; Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Na He
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, China; Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Xue He
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, China; Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Yongri Ouyang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Hong Wang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Bo Wang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, China; Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Dongya Yuan
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China; Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, China; Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China.
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